PDB-2h76: Crystal Structure of Thioredoxin Mutant D10E in Hexagonal (p61) S...

ID or keywords:

Entry

Database: PDB / ID: 2h76

Title

Crystal Structure of Thioredoxin Mutant D10E in Hexagonal (p61) Space Group

Components

Thioredoxin

Keywords

LYASE / Alpha Beta / Electron transport

Function / homology

Function and homology information

DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.25 Å

Authors

Gavira, J.A. / Godoy-Ruiz, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.

Citation

Journal: To be Published
Title: Crystal Structure of Thioredoxin Mutant D10E in Hexagonal (p61) Space Group
Authors: Godoy-Ruiz, R. / Gavira, J.A. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.

History

Deposition	Jun 1, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 15, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	May 2, 2012	Group: Structure summary
Revision 1.4	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5	Oct 20, 2021	Group: Database references / Derived calculations / Experimental preparation Category: database_2 / exptl_crystal_grow ...database_2 / exptl_crystal_grow / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal_grow.method / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2h76.cif.gz	59.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2h76.ent.gz	44.4 KB	Display	PDB format
PDBx/mmJSON format	2h76.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2h76_validation.pdf.gz	443.6 KB	Display	wwPDB validaton report
Full document	2h76_full_validation.pdf.gz	445.3 KB	Display
Data in XML	2h76_validation.xml.gz	11.4 KB	Display
Data in CIF	2h76_validation.cif.gz	15.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h7/2h76 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/2h76	HTTPS FTP

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Related structure data

Related structure data	2trxS 1zzy 2fch 2fd3 2h6x 2h6y 2h70 2h71 2h72 2h73 2h74 2h75 2h7z S: Starting model for refinement
Similar structure data	2h6x-1 2tir-d 5hr1-4 2h6z-1 2xbq-3 2h73-1 2fch-5 5hr3-1 2h71-1 2eir-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#91 - Jul 2007 Thymine Dimers similarity (5) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (4)

Deposited unit

A: Thioredoxin

B: Thioredoxin

hetero molecules

23.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Thioredoxin

hetero molecules

defined by author
11.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Thioredoxin

defined by author
11.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.170, 103.170, 41.834
Angle α, β, γ (deg.)	90.00, 90.00, 120
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Thioredoxin Mass: 11701.413 Da / Num. of mol.: 2 / Mutation: D10E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA / Plasmid: pTK100 / Production host: Escherichia coli (E. coli) / Strain (production host): JF521 / References: UniProt: Q2M889, UniProt: P0AA25*PLUS
#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.52 %
Crystal grow	Temperature: 277 K / Method: counter-diffusion / pH: 3.5 Details: 60% (v/v) MPD, HEPES 15 mM pH 4.1, Ac2Cu 1mM, AcNa 15m, pH 3.5, Counter-diffusion, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
Detector	Type: BRUKER SMART 6000 / Detector: CCD / Date: Feb 20, 2006 / Details: Montel Optics
Radiation	Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.25→51.58 Å / Num. all: 12308 / Num. obs: 12308 / % possible obs: 99.9 % / Redundancy: 28.93 % / B_iso Wilson estimate: 37.35 Å² / R_sym value: 0.0241 / Net I/σ(I): 27.13
Reflection shell	Resolution: 2.25→2.3 Å / Redundancy: 22.28 % / Mean I/σ(I) obs: 6.46 / Num. unique all: 779 / R_sym value: 0.1501 / % possible all: 100

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
SAINT		data scaling
MOLREP		phasing
REFMAC	refmac_5.2.0019	refinement
PDB_EXTRACT	1.7	data extraction
PROTEUM PLUS	2	data reduction
SADABS		data scaling
XPREP		data reduction
Coot		model building
MolProbity		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2TRX

2trx

Resolution: 2.25→51.58 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.905 / WR_factor R_free: 0.256 / WR_factor R_work: 0.189 / SU B: 13.361 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.268	1186	9.797 %	Random
R_work	0.1954	-	-	-
all	0.202	12308	-	-
obs	0.202	12106	98.447 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 26.62 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.082 Å²	-1.041 Å²	0 Å²
2-	-	-2.082 Å²	0 Å²
3-	-	-	3.123 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→51.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1640	0	16	99	1755

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	1750
X-RAY DIFFRACTION	r_angle_refined_deg	1.403	1.994	2386
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.783	5	228
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.268	26.25	72
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.798	15	314
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.691	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	275
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1290
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	736
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	1140
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.397	0.2	116
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.183	0.2	21
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.232	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	1.232	2	1128
X-RAY DIFFRACTION	r_mcangle_it	1.832	3	1761
X-RAY DIFFRACTION	r_scbond_it	1.134	2	710
X-RAY DIFFRACTION	r_scangle_it	1.648	3	617

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	% reflection obs (%)
2.25-2.308	0.314	66	0.235	799	0.242	892	96.973
2.308-2.372	0.257	78	0.223	813	0.227	897	99.331
2.372-2.44	0.336	67	0.23	742	0.24	836	96.77
2.44-2.515	0.359	105	0.226	708	0.242	828	98.188
2.515-2.597	0.309	86	0.224	710	0.233	811	98.15
2.597-2.688	0.298	77	0.212	675	0.22	765	98.301
2.688-2.789	0.308	78	0.204	684	0.214	775	98.323
2.789-2.903	0.4	56	0.214	630	0.227	702	97.721
2.903-3.032	0.296	73	0.223	614	0.231	698	98.424
3.032-3.179	0.267	68	0.19	599	0.198	675	98.815
3.179-3.35	0.276	58	0.187	554	0.196	618	99.029
3.35-3.553	0.265	59	0.189	541	0.196	606	99.01
3.553-3.797	0.206	62	0.167	505	0.171	571	99.299
3.797-4.099	0.197	56	0.16	468	0.164	527	99.431
4.099-4.487	0.224	51	0.164	443	0.17	494	100
4.487-5.012	0.217	38	0.164	398	0.169	436	100
5.012-5.779	0.266	41	0.197	361	0.204	402	100
5.779-7.055	0.257	29	0.222	311	0.225	340	100
7.055-9.886	0.25	25	0.186	234	0.192	260	99.615
9.886-51.58	0.471	13	0.258	131	0.271	164	87.805

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.2033	-1.9468	0.6431	4.8097	-3.1504	21.1891	0.2211	0.3566	-0.2838	-0.3991	-0.1273	-0.3317	1.088	0.2973	-0.0937	0.0486	0.0147	0.0468	0.0951	-0.0442	0.135	-20.064	3.486	0.05
2	10.8694	-8.43	7.2003	10.8265	2.248	19.0743	-0.0798	-0.7416	0.7543	1.0499	0.4475	0.0772	0.1709	0.3962	-0.3678	0.0715	-0.0219	0.005	0.0748	-0.0014	0.1263	-16.881	10.378	8.333
3	3.6921	3.424	-0.6119	4.9171	-0.0683	2.2117	0.0227	0.0218	-0.137	0.1811	0.0179	-0.1206	0.016	0.1019	-0.0406	0.0639	0.0175	-0.0017	0.0558	0.0003	0.1203	-24.805	9.175	2.852
4	6.1484	3.0422	-5.6752	6.2776	-1.8895	10.3949	0.0993	0.5446	-0.3673	-0.2575	0.2305	0.3495	0.1108	-0.2393	-0.3299	-0.0011	-0.0038	-0.0245	0.0566	-0.0468	0.1693	-32.881	2.399	-4.8
5	9.0664	-0.9537	5.566	20.6331	-5.4632	5.5536	-0.0014	1.1082	-0.659	-1.1126	0.0396	-0.3321	0.0291	0.1241	-0.0382	0.0105	-0.0066	0.0369	0.141	-0.0703	-0.0154	-23.068	10.65	-12.303
6	1.5871	-0.4834	-0.1678	3.9121	-1.3432	0.5341	0.024	-0.1912	-0.1227	0.4881	0.1335	0.0018	-0.0103	0.1307	-0.1574	0.0941	0.0016	0.0069	0.0574	0.0041	0.0835	-26.044	6.371	8.275
7	3.7985	-0.9631	0.1161	0.2466	-0.0337	0.0114	-0.0687	-0.2436	-0.1664	0.0437	0.0317	0.2403	0.1849	0.0931	0.0371	0.0723	-0.0217	0.0679	0.0233	-0.0108	0.1053	-34.834	11.748	7.83
8	2.8874	3.3569	-2.8761	3.9566	-2.8261	7.8322	0.0316	-0.3133	0.6805	-0.2829	-0.236	-0.0932	-0.1949	0.103	0.2045	0.0337	0.0206	0.0074	0.0205	-0.0005	0.1629	-24.001	19.215	0.943
9	2.6723	2.3245	2.7068	4.6443	0.0687	4.7342	0.1457	0.3148	0.0694	-0.157	0.2507	0.2225	0.2503	0.0363	-0.3964	-0.0053	0.0166	-0.0101	0.0641	-0.0611	0.1666	-35.779	12.307	-5.298
10	1.192	4.1427	2.7719	20.4721	3.5029	12.6344	0.117	0.3393	0.1199	-0.7642	-0.1571	-0.3545	-0.7082	-0.0672	0.0402	-0.0051	0.0334	0.0014	0.037	-0.0143	0.1291	-30.871	18.765	-8.998
11	8.1815	-1.0694	0.3932	6.7129	-1.0039	16.7058	0.0647	-0.2241	-0.4268	0.3296	-0.195	0.7862	-0.0873	-0.1264	0.1302	0.0318	0.046	0.0553	-0.059	-0.1001	0.2644	-42.223	37.101	7.251
12	3.0136	-5.1843	0.3457	10.8689	-0.614	0.0399	0.1973	0.1287	0.4857	-0.3238	-0.141	0.0582	0.0499	0.0012	-0.0563	0.0666	0.0427	0.081	-0.0034	-0.0592	0.1905	-36.816	42.783	3.193
13	1.2021	-0.4543	-0.3618	5.0263	0.2231	0.5127	-0.0464	-0.1777	0.1202	0.4956	0.0405	0.3236	-0.0017	0.0551	0.006	0.0943	-0.0226	0.0925	0.0168	-0.026	0.1008	-34.799	24.671	9.497
14	11.6619	-4.2439	0.6159	20.3069	2.7374	0.5	-0.4924	-0.9854	0.2589	2.6658	0.7201	0.2516	0.5819	0.4376	-0.2276	0.3711	0.0408	0.0039	0.0557	-0.0722	-0.0872	-26.637	36.657	15.792
15	19.0427	12.5855	6.9562	15.1576	6.5883	7.7717	0.0553	-0.2237	0.8128	0.3643	-0.0474	0.6895	-0.4728	0.1261	-0.0079	0.0972	0.0568	0.0883	-0.0382	-0.0367	0.0697	-34.956	35.74	8.394
16	17.3921	2.3395	-7.8594	4.7471	-6.0751	9.2323	0.3082	0.459	-0.0664	-0.4617	-0.2247	0.756	-0.176	-0.0996	-0.0836	0.1615	0.0315	-0.037	-0.1056	-0.0778	0.0824	-41.302	30.01	-2.671
17	3.2588	2.8617	-1.267	7.7891	-1.3805	0.5062	0.3009	0.2633	0.2796	-0.476	-0.3953	0.4745	0.0437	-0.0994	0.0945	0.1003	0.0333	0.0183	0.0379	0.0007	0.115	-32.334	30.163	-0.184
18	9.566	-6.3799	2.4037	14.9632	-5.4924	6.5772	0.3552	0.4821	0.4581	-0.2881	-0.1772	-0.0059	-0.3686	-0.4047	-0.1779	0.0398	0.0515	0.0846	0.0663	-0.0089	0.0686	-28.456	36.267	-0.766
19	3.9454	1.7742	0.089	11.7801	-9.0757	11.1896	0.0884	-0.4111	-0.2245	0.6872	0.0898	-0.2916	-0.3139	0.5157	-0.1781	0.083	0.0138	-0.0066	0.1107	-0.092	0.0127	-20.883	31.489	8.925
20	23.3211	0	0	33.6583	0	21.7294	-0.1163	0.1158	1.2494	1.1459	0.6593	-2.3467	-1.2043	-0.1381	-0.5429	0.1163	-0.0664	-0.0257	-0.0071	-0.0923	0.0424	-20.985	40.43	5.488

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	1 - 9	1 - 9
2	2	A	A	10 - 14	10 - 14
3	3	A	A	15 - 31	15 - 31
4	4	A	A	32 - 46	32 - 46
5	5	A	A	47 - 53	47 - 53
6	6	A	A	54 - 69	54 - 69
7	7	A	A	70 - 78	70 - 78
8	8	A	A	79 - 86	79 - 86
9	9	A	A	87 - 100	87 - 100
10	10	A	A	101 - 108	101 - 108
11	11	B	B	2 - 13	2 - 13
12	12	B	B	14 - 25	14 - 25
13	13	B	B	26 - 43	26 - 43
14	14	B	B	44 - 49	44 - 49
15	15	B	B	50 - 60	50 - 60
16	16	B	B	61 - 72	61 - 72
17	17	B	B	73 - 81	73 - 81
18	18	B	B	82 - 94	82 - 94
19	19	B	B	95 - 102	95 - 102
20	20	B	B	103 - 108	103 - 108

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